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from ete3 import PhyloTree
# Loads a gene tree and its corresponding species tree. Note that
# species names in sptree are the 3 firs letters of leaf nodes in
# genetree.
gene_tree_nw = '((Dme_001,Dme_002),(((Cfa_001,Mms_001),((Hsa_001,Ptr_001),Mmu_001)),(Ptr_002,(Hsa_002,Mmu_002))));'
species_tree_nw = "((((Hsa, Ptr), Mmu), (Mms, Cfa)), Dme);"
genetree = PhyloTree(gene_tree_nw)
sptree = PhyloTree(species_tree_nw)
print(genetree)
# /-Dme_001
# /--------|
# | \-Dme_002
# |
# | /-Cfa_001
# | /--------|
#---------| | \-Mms_001
# | /--------|
# | | | /-Hsa_001
# | | | /--------|
# | | \--------| \-Ptr_001
# \--------| |
# | \-Mmu_001
# |
# | /-Ptr_002
# \--------|
# | /-Hsa_002
# \--------|
# \-Mmu_002
#
# Let's reconcile our genetree with the species tree
recon_tree, events = genetree.reconcile(sptree)
# a new "reconcilied tree" is returned. As well as the list of
# inferred events.
print("Orthology and Paralogy relationships:")
for ev in events:
if ev.etype == "S":
print('ORTHOLOGY RELATIONSHIP:', ','.join(ev.inparalogs), "<====>", ','.join(ev.orthologs))
elif ev.etype == "D":
print('PARALOGY RELATIONSHIP:', ','.join(ev.inparalogs), "<====>", ','.join(ev.outparalogs))
# And we can explore the resulting reconciled tree
print(recon_tree)
# You will notice how the reconcilied tree is the same as the gene
# tree with some added branches. They are inferred gene losses.
#
#
# /-Dme_001
# /--------|
# | \-Dme_002
# |
# | /-Cfa_001
# | /--------|
# | | \-Mms_001
#---------| /--------|
# | | | /-Hsa_001
# | | | /--------|
# | | \--------| \-Ptr_001
# | | |
# | | \-Mmu_001
# \--------|
# | /-Mms
# | /--------|
# | | \-Cfa
# | |
# | | /-Hsa
# \--------| /--------|
# | /--------| \-Ptr_002
# | | |
# | | \-Mmu
# \--------|
# | /-Ptr
# | /--------|
# \--------| \-Hsa_002
# |
# \-Mmu_002
#
# And we can visualize the trees using the default phylogeny
# visualization layout
genetree.show()
recon_tree.show()
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